Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
ARID1B

Cell type

Cell type Class
Neural
Cell type
Neural crest cells
NA
NA

Attributes by original data submitter

Sample

source_name
Control_Line_2 (SV20 line)
cell type
Cranial_Neural_Crest_Cells_DAY5
antibodies
ARID1B Abcam ab57461

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNA-seq Cells were lysed in Tri-reagent (Zymo research) and total RNA was extracted using Quick-RNA Miniprep kit (Zymo research). RNA libraries were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® and NEBNext® UltraTM II DNA Library Prep Kit for Illumina® according to the manufacturer's instructions (New England Biolabs). 1 μg of total RNA input was used for each library ATAC-seq: 50000 cells per condition were processed as described in the original ATAC-seq protocol paper (Buenrostro et al 2013) ChIP-seq: Barcoded libraries were made with NEB ULTRA II DNA Library Prep Kit for Illumina, and sequenced on Illumina NextSeq 500, producing 75bp SE reads.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
26413713
Reads aligned (%)
94.6
Duplicates removed (%)
9.2
Number of peaks
1061 (qval < 1E-05)

hg19

Number of total reads
26413713
Reads aligned (%)
93.9
Duplicates removed (%)
10.3
Number of peaks
1023 (qval < 1E-05)

Base call quality data from DBCLS SRA